History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries—a time of agricultural intensification well before the Inka and Spanish conquests—and then between the 13th century and today—a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.

Quinoa (Chenopodium quinoa, 2n = 4x = 36, AABB subgenomes) is a highly nutritious crop with the potential to diversify global diets and alleviate malnutrition. It is also adaptable for production in soils increasingly affected by salinization and water scarcity. Quinoa was domesticated and artificially selected as a crop within the Andes Mountains, the geographically isolated Mediterranean climate zone of coastal Chile, and along the northwestern fringe of the Argentine dry Pampas. In addition, there is now abundant information regarding the wild species that were its immediate ancestors and which should be viewed as its secondary and tertiary breeding gene pools. These same ancestors contributed to independent domestications of the other forms of “quinoa” in ancient Mesoamerica and eastern North America from a common AABB ancestor-species, C. berlandieri, known commonly as pitseed goosefoot (PG). This review explores the biogeography of the diploid and polyploid relatives of the AABB allotetraploid goosefoot complex (ATGC). The seven or more ecotypes of PG, including the South American taxon C. hircinum, or avian goosefoot (AG), contain broad genetic variability, and some can be used directly as crossing partners in making quinoa breeding populations. Of the extant diploid relatives, C. subglabrum (SMG) is most closely related to the original maternal subgenome A of PG, while C. suecicum (SWG) or C. ficifolium (FG) are most closely related to paternal subgenome B. These and the other AA and BB diploids are valuable model organisms for locating and modifying genes of interest and their expression, the ultimate goals being to increase quinoa’s yield potential, improve its nutritional attributes, explore value-adding industrial uses, and enhance quinoa’s already formidable mechanisms to resist environmental stresses. This review is an update on the current state of quinoa breeding, with an emphasis on the value of wild genetic resources for quinoa improvement. It provides a comprehensive review of the scientific literature for scientists interested in adding quinoa to their breeding program.

Quinoa (Chenopodium quinoa, 2n = 4x = 36, AABB subgenomes) is a highly nutritious crop with potential to diversify global diets and alleviate malnutrition. It is also adaptable for production in soils increasingly affected by salinization and water scarcity. Quinoa was domesticated and artificially selected as a crop within the Andes Mountains, the geographically isolated Mediterranean climate zone of coastal Chile, and along the northwestern fringe of the Argentine dry Pampas. In addition, there is now abundant information regarding the wild species that were its immediate ancestors and which should be viewed as its secondary and tertiary breeding gene pools. These same ancestors contributed to independent domestications of the other forms of “quinoa” in ancient Mesoamerica and eastern North America from a common AABB ancestor-species, C. berlandieri, known commonly as pitseed goosefoot (PG). This review explores the biogeography of the diploid and polyploid relatives of the AABB allotetraploid goosefoot complex (ATGC). The seven or more ecotypes of PG, including the South American taxon C. hircinum or avian goosefoot, contain broad genetic variability and some can be used directly as crossing partners in making quinoa breeding populations. Of the extant diploid relatives, C. subglabrum is most closely related to the original maternal subgenome A of PG, while C. suecicum or C. ficifolium are most closely related to paternal subgenome B. These and the other AA and BB diploids are valuable model organisms for locating and modifying genes of interest and their expression, the ultimate goals being to increase quinoa’s yield potential, improve its nutritional attributes, explore value-adding industrial uses, and enhance quinoa's already formidable mechanisms to resist environmental stresses.

The Hsp20 protein family, essential in heat stress responses across all organisms, is part of the heat shock protein (Hsp) superfamily, recognized for its conserved alpha-crystallin domain (ACD). Hsp20s are the smallest proteins in the superfamily and primarily assist in protein refolding during stress and developmental processes. We present an in silico characterization of the Hsp20 gene family in Chenopodium quinoa (2n = 4x = 36) using an integrative approach. Quinoa is well known for its global contributions to food production and tolerance to various abiotic stresses. We identified 69 CqHsp20 genes that exhibit a well-conserved evolutionary pattern, characterized by a balanced copy number distributed symmetrically across 19 homeologous pairs in both subgenomes (A and B), with localized expansions driven by tandem duplications on eight chromosomes. High sequence identity in contiguous gene pairs and Ka/Ks ratios consistently below 1 (0.14–0.84) mathematically demonstrate that strict purifying selection has maintained the structural and sequence integrity of these genes since the ancestral polyploidization event. The phylogenetic analysis grouped CqHsp20 into two main clusters, splitted into four sub-clusters based on peptides’ cellular localization, consistent with a characteristic gene structure and conserved motif analysis, which may reflect the evolutionary trajectory and functional specialization of the Hsp20 family in plants. The integration of transcriptomic data from published experiments enabled us to detect a cluster of putatively ubiquitously expressed CqHsp20, as well as other groups that showed differential responses across abiotic stress conditions. The pattern shows that more genes exhibit higher transcription abundance under drought and salinity than under heat, key adaptive traits underlying quinoa’s known ecological versatility. Some of these genes, which are undetectable or have low abundance under heat stress, encode organelle-targeting peptides, a phenomenon not reported in other model plant studies. Differential expression analysis revealed a highly transcribed sub-cluster where six out of seven of nuclear CqHsp20 genes were active in aerial tissue during initial heat stress, with a specific cohort of four genes (CQ025082, CQ031384, CQ041158, and CQ055373) maintaining significant upregulation ($|{log}_2\mathrm{Fold}\mathrm{Change}|\ge 1.0$, $\mathrm{padj}<0.05$) under prolonged and simultaneous shoot/root exposure. Varying expression within CqHsp20 homologous and paralogs supports the idea that gene duplication creates genomic diversity, facilitating adaptation to variable extreme environments. However, while theoretical and in silico analysis provide valuable insight into quinoa Hsp20 response, empirical data are essential to unequivocally understand how these gene expression variations affect quinoa response to abiotic stressors.

The Hsp20 protein family, recognized in all organisms for its chaperone activity in the heat-stress response, is part of the Heat Shock Protein (Hsp) superfamily, defined by a conserved alpha-crystallin domain (ACD). Hsp20s are the smallest proteins in the superfamily (mostly between 15 and 22 kDa) and assist in protein refolding during stress and developmental processes. In this study, we characterize the Hsp20 gene family in Chenopodium quinoa (2n = 4x = 36) using an integrative omic approach. C. quinoa is well known for its global contributions to food production and tolerance to various abiotic stresses. We identified 69 CqHsp20 genes distributed across the nine chromosomes of each subgenome (A and B), organized mainly into homologous pairs, with paralogs on eight chromosomes, likely from tandem duplications, suggesting a well-conserved evolutionary pattern within the species. The phylogenetic analysis grouped CqHsp20 proteins into two main clusters, split into four sub-clusters based on peptides’ cellular localization, consistent with a characteristic gene structure and conserved motif analysis. The integration of transcriptomic data from published experiments enabled us to detect a cluster of putatively ubiquitously expressed CqHsp20, as well as other groups that showed differential responses across abiotic stress conditions. The pattern shows more genes with transcriptional activity under drought and salinity than under heat, key adaptive traits underlying quinoa’s known ecological versatility. Some of these genes, with null or low transcriptional activity under heat stress, encode organelle-targeting peptides, a phenomenon not reported in other model plant studies. Varying expression within CqHsp20 homologous and paralogs supports the idea that gene duplication creates genomic diversity, facilitating adaptation to variable extreme environments. However, while theoretical and in silico analysis provide valuable insight into quinoa Hsp20 response, empirical data are essential to unequivocally understand how these gene expression variations affect quinoa response to abiotic stressors.

Several species within the genus Valeriana are globally recognized for their medicinal properties. However, their increasing economic value has led to overharvesting of natural populations, posing a serious threat to their long-term sustainability. Effective strategies for conservation and rational use require accurate species identification and robust assessment of genetic diversity, yet molecular tools for these purposes remain scarce in genus Valeriana . In this study, we developed microsatellite markers based on transcriptomic data from Valeriana clarionifolia . A total of 2216 putative simple sequence repeat (SSR) loci were identified from a transcriptome deposited in the NCBI Sequence Read Archive (BioProject PRJNA950387), and primers were designed for 691 candidate markers. From 60 selected loci, twelve polymorphic SSR markers were isolated and evaluated in V. carnosa Sm., V. clarionifolia Phil., V. gaimanensis N. Nagh., V. moyanoi Speg., and V. philippiana Briq. Mean cross-species transferability and polymorphism were 91.67% and 83.34%, respectively. The number of alleles per locus ranged from four to fourteen, with an average polymorphism information content (PIC) of 0.67. Among the evaluated loci, primer valcla4800 showed the highest discriminatory capacity (PIC = 0.89). This study represents the first genomic characterization of native Valeriana species from Patagonia and demonstrates the high transferability and informativeness of transcriptome-derived SSR markers within the genus. The molecular tools generated here provide valuable resources for species identification, genetic diversity assessment, and selection of plant material, supporting conservation efforts and sustainable use of medicinal plants.